Dr Lawrence Cohen resigned after being asked to step down and an investigation is underway, reported ABC News.
"BREAKING: Medical director of Yorkville Endoscopy where #JoanRivers went to cardiac arrest is out. He is no longer performing procedures at the clinic."
Rivers had a cardiac arrest while undergoing an outpatient procedure on her vocal cords on August 28 and was later pronounced dead on September 4 at New York City's Mount Sinai Hospital.
There were reports in the US media that an unplanned throat biopsy led to her untimely death at the age of 81.